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Ethanol Production by Fermentation of Various Sweet-Stalk Sorghum Juices Using Various Yeast Strains Widianto, Donny; Arofatullah, Akbar; Yuwono, Triwibowo; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

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The ethanol production by fermentation of sweet-stalk sorghum juice is affected by the juice composition and the capability of the yeast strain to ferment it. Eight yeast strains were tested on their growth and ethanol fermentation abilities in sweet-stalk sorghum juices extracted from three cultivars of sweet sorghum. The best specific growth rate of the yeast strains grown aerobically in the yeast extract peptone dextrose (YEPD) broth and the sweet-stalk sorghum juices of KCS105, FS501, and FS902 cultivars, were achieved by OUT7903, OUT7913, OUT7903, and OUT7027 yeast strains, respectively. However, the best specific CO2 evolution rate of the yeast strain during fermentation of the juices was achieved by OUT7027 yeast strains. The highest ethanol concentration, ethanol yield, and sugar conversion efficiency (SCE) were obtained by strain OUT7921 when it was employed to ferment sweet-stem sorghum juice of FS902 cultivar. It was also observed that the juice extracted from sweet-stalk sorghum of FS902 cultivar is the most suitable medium for all yeast strains to achieve their best fermentation abilities. Thus, it is likely that the growth and ethanol production ability of a yeast strain in sweet-stalk sorghum juice depend on the physiological responses of the yeasts to nutrientcomposition of the sorghum juice and the sorghum cultivar from which the juice was extracted.Key words : Sweet-stalk sorghum juice, ethanol, fermentation, yeast

Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Wedhastri, Sri; Fardhani, Dinar Mindrati; Kabirun, Siti; Widada, Jaka; Widianto, Donny; Evizal, Rusdi; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene.Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max

Cloning of Thermostable DNA Polymerase Gene from a Thermophilic Brevibacillus sp. Isolated from Sikidang Crater, Dieng Plateu, Central Java Witasari, Lucia Dhiantika; Prijambada, Irfan Dwidya; Widada, Jaka; Arif Wibawa, Dionysius Andang
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

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Thermostable DNA polymerase has an important role for amplifying small amount of DNA through polymerase chain reaction (PCR). Thermophillic bacteria Brevibacillus sp. was isolated from Sikidang Crater, Dieng Plateu, Central Java. Previous study showed that crude protein of the isolate could be used in PCR. Unfortunately, like most native thermostable enzymes, the thermostable DNA polymerase of the isolate is synthesized in a very low level and therefore is cumbersome to purify. The purpose of this research is to clone thermostable DNA polymerase gene of the isolate. The DNA polymerase gene was amplified by means of PCR using spesific primers. The amplified fragment was then isolated, purified, and ligated into the pGEM-T cloning vector. The recombinant plasmid was then transformed to competent E. coli JM109 cells using heat shock method. The cloned thermostable DNA polymerase gene from the thermophilic isolate was then characterized for its nucleotide base sequence. The result showed that the DNA Pol I gene was successfully be amplified from the isolate DNA genom, resulting in ± 2,7 kb DNA fragment in length. Sequence analysis of segment of targeted gene showed high similarity to that of thermostable DNA polymerase genes from other Bacillus.Key words : Thermostable DNA Pol I, Brevibacillus sp., PCR, cloning

Ethanol Fermentation on Mixed Sugars Using Mixed Culture of Two Yeast Strains ., Jasman; Prijambada, Irfan Dwidya; Hidayat, Chusnul; Widianto, Donny
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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The objective of this study was to evaluate the use of mixed cultures of the recommended yeast strainsfrom a previous study on ethanol fermentation using a substrate mixture consisting of sucrose, glucose, andfructose. There were three mixed (combination) cultures namely OUT7096/OUT7913, OUT7096/OUT7921,and OUT7913/OUT7921. The fermentation medium contained sugar mixture consisting of glucose, fructose,and sucrose with a composition generally close to the composition of sugars in sweet sorghum juice. Overall,fermentation is carried out in two stages. First fermentation was performed using the three mixed culturesto determine the best combination based on the concentration of ethanol produced and the concentration ofresidual sugar. Second fermentation was conducted using the best mixed culture obtained from the fi rst stage.This second stage was intended to describe the pattern of the changes in the concentration of ethanol, sugarsand biomass during the fermentation progresses and to determine some kinetic parameters namely ethanolyield (Yp/s), growth yield (Yx/s) and specifi c growth rate (μ). The results of the fi rst fermentation showed thatthe best mixed culture was OUT7913/OUT7921 and the subsequent fermentation using this culture providethe highest ethanol yield (Yp/s) = 0.47 g.g-1 that was reached at 53rd hour, growth yield (Yx/s) = 0.425 g.g-1, andμ = 0.12 hour-1.Keywords : fermentation, ethanol, mixed culture, mixed sugar

Diversity of Dibenzofuran-Utilizing Bacteria Isolated by Direct-Plating and Enrichment Methods Prijambada, Irfan Dwidya; Widada, Jaka; Kusumaningtyas, Pintaka; Suryawan, Dhani
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

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The effect of enrichment bias on the diversity of Dibenzofuran (DBF)-degrading bacteria recovered from soil was evaluated by direct plating, plating after in-soil adaptation, and plating after batch culture enrichment. Among colonies appeared on Bushnell Haas agar with DBF as the sole carbon source, 119 colonies (49, 38, and 32 from direct plating, plating after in-soil adaptation, and plating after batch culture enrichment, respectively) were arbitrarily selected based on the appearance of the colonies. Total DNA were then extracted from the rest of the colonies and analyzed for their diversity using Ribosomal Intergenic Spacer Analysis (RISA). Number of DNA bands obtained from direct plating was higher than the ones obtained after in-soil enrichment and batch culture enrichment. The RISA bands obtained from direct plating were also found to be distributed more evenly than the ones obtained after in-soil enrichment and batch culture enrichment. Dominant bands were observed on RISA from samples obtained after in-soil enrichment and batch culture enrichment. Out of 119, only 9 isolates were consistently able to grow on Bushnell-Haas broth with DBF as the sole carbon source as indicated by broth turbidity. All of the isolates were obtained from soil samples which were enriched in a batch culture. Some of the isolates were able to degrade more then 80 % DBF in the minimal medium.

Konstruksi Open Reding Frames (ORF) Artifisial Berukuran 798-bp yang Menyandi Protein dengan Urutan Asam Amino Acak Prijambada, Irfan Dwidya; Al-Awally, Khotibul Umam; Rohman, Muhammad Saifur; Artama, Wayan
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 9, No 1 (2004): February 2004
Publisher : Universitas Atma Jaya Yogyakarta

Penyusunan pustaka dari open reading frames (ORF) buatan yang tersusun atas 798 bp (pasangan basa), 576Â di antaranya tersusun secara acak, yang mampu menyandi 266 asam amino telah berhasil dilakukan. Dalam upaya penyusunan tersebut diperoleh 32 transforman,Â lima di antaranya membawa ORF buatan. Dari kelima transforman yang membawa ORF buatan tersebut, hanya satu transforman yang mampu berekspresi dan menyandi suatu protein. Protein yang dihasilkan memiliki ukuran 17 kDa, berukuran lebih kecil daripada ukuran yang diharapkan yaitu 29 kDa.

BACTERIAL Cr (VI) REDUCTION AND ITS IMPACT IN BIOREMEDIATION Pramono, Ali; Rosariastuti, MMA Retno; Ngadiman, N; Prijambada, Irfan D
Jurnal Ilmu Lingkungan Vol 11, No 2 (2013): Oktober 2013
Publisher : School of Postgraduate Studies, Diponegoro Univer

ABSTRACTChromium is hazardous pollutant for ecosystem caused chromium especially inhexavalent form is very toxic, has high solubility and mobility, teratogenicity, mutagenicity andcarcinogenicity to living system related with its oxiding power. Remediation of soilcontaminated of heavy metals was important caused soil as medium for food producing.Conventional methods for heavy metals remediation consist of physical and chemical processbut these applications were costly and less effective. One of the remediation technologies is theusing living organisms such as microorganisms, because they have ability to reduce Cr(VI) intonon toxic form, Cr(III). The aims of this research were to evaluate the reduction activity ofrhizobacterial isolate and to identify the isolate which take a role in reducing chromiumabsorption by plant. The results showed that Isolate 39 was able to grow on LB mediumcontaining 200 ppm Cr(VI). Isolate 39 reduced Cr(VI) up to 15 ppm concentration level inminimal medium. Isolate 39 has ability to reduce Cr(VI) both at growing cells and resting cellsconditions up to 100% and 51% within 18 hours, respectively. Isolate 39 increased thephytostabilization ability of chromium by Zea mays at 30 days after seeding 3.8 timescompared than control. Based on physiological characteristics and partial sequencing of 16SrRNA gene, Isolate 39 was identified as Agrobacterium sp.Key words : Agrobacterium sp, hexavalent chromium, reduction, Zea mays

PENGARUH BAHAN ORGANIK DAN SUHU PENGERINGAN TERHADAP KETAHANAN HIDUP ASPERGILLUS NIGER DALAM PUPUK PELET BIO-FOSFAT Sastro, Yudi; Widianto, Donny; Prijambada, Irfan D.
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 12, No 2 (2007): June 2007
Publisher : Universitas Atma Jaya Yogyakarta

This research was aimed to investigate the effect of organic matter and drying temperature on Aspergillus niger survivability in the rock phosphate pellet fertilizer namely bio-phosphate. The research was arranged by a completely randomized design 3x3x6. Addition of the mixing of tapioca waste, rice bran, and starch (BOC) and the humic substance (BH) in the bio-phosphate, and its drying temperature (SP) were the treatments. Aspergillus niger inoculums survivability in the bio-phosphate was determined using plating methods. The result showed that the addition of BOC decreased amount of A. niger in the bio-phosphate up to 28.0%, while the BH increased the amount of A. niger up to 24.4%. The ideal drying temperature of bio-phosphate pellet fertilizer was 600C.

The Effect of Rock Phosphate and Level of Inoculums on The Survivability of Aspergillus niger and Its Solubilization Ability When Pelleted With Rock Phosphate Yudi Sastro; Donny Widianto; Irfan D Prijambada
Jurnal Ilmu Tanah dan Lingkungan Vol 7 No 2 (2005): Jurnal Ilmu Tanah dan Lingkungan
Publisher : Departemen Ilmu Tanah dan Sumberdaya Lahan, Fakultas Pertanian, IPB University

The study is intended to examine the survival of Aspergillus niger and its phosphate solubilizing ability when pelletedwith rock phosphate. An A. niger YD 17 obtainedfrom the Laboratory of Microbiology. Faculty of Agriculture, Gadjah MadaUniversity was used. The pellet was made by mixing rock phosphate (80%) with organic matter (J 3. 9% waste of tapioca. 6% rice bran, and 1% starch) and spore of A. niger. The experimental design was the Complete Randomized Design 5x4 with 3 replicatiOns. The first factor was sources of rock phosphate (Christmas Island. Jordan, China, Ciamis, and Madura). The secondfactor was the number ofinoculums i.e. control without inoculums, 107 • J(t and J(t cfu.g·'. The colony of A. niger that formed at medium of potatoes dextrose agar (PDA) and the amount of soluble phosphorus in the Pikovskaya liquid medium were parameters. Experimental results indicated that sources of rock phosphate and the number of inoculums itif1uence the A. niger survivability and its phosphorus solubilizing ability. Rock phosphate from Ciamis gave the best support for fungus survival and rock phosphate from Christmas Island was the best substrate for phosphate solubilization. The highest soluble phosphate was achieved by ul inoculums.

Ethanol Production by Fermentation of Various Sweet-Stalk Sorghum Juices Using Various Yeast Strains Donny Widianto; Akbar Arofatullah; Triwibowo Yuwono; Irfan Dwidya Prijambada
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

The ethanol production by fermentation of sweet-stalk sorghum juice is affected by the juice composition and the capability of the yeast strain to ferment it. Eight yeast strains were tested on their growth and ethanol fermentation abilities in sweet-stalk sorghum juices extracted from three cultivars of sweet sorghum. The best specific growth rate of the yeast strains grown aerobically in the yeast extract peptone dextrose (YEPD) broth and the sweet-stalk sorghum juices of KCS105, FS501, and FS902 cultivars, were achieved by OUT7903, OUT7913, OUT7903, and OUT7027 yeast strains, respectively. However, the best specific CO2 evolution rate of the yeast strain during fermentation of the juices was achieved by OUT7027 yeast strains. The highest ethanol concentration, ethanol yield, and sugar conversion efficiency (SCE) were obtained by strain OUT7921 when it was employed to ferment sweet-stem sorghum juice of FS902 cultivar. It was also observed that the juice extracted from sweet-stalk sorghum of FS902 cultivar is the most suitable medium for all yeast strains to achieve their best fermentation abilities. Thus, it is likely that the growth and ethanol production ability of a yeast strain in sweet-stalk sorghum juice depend on the physiological responses of the yeasts to nutrientcomposition of the sorghum juice and the sorghum cultivar from which the juice was extracted.Key words : Sweet-stalk sorghum juice, ethanol, fermentation, yeast

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